Everytime I try to open any of these files, my Atom freezes and locks up, getting prompted after a minute or two to “wait or close.” If I click wait, which I have many times, it continues to stay frozen.

Since it says “atom core”, I don’t think this is a package that I can upgrade.

When loading Atom in safe mode, I don’t get the deprecation warning… Hence, the need to load my plugins to see what is going on.

It is saying that the environment package is deprecated. So you should uninstall the environment package like it says in the README, the functionality of the package was obviated by a pull request to Atom itself quite a while ago.